đŸ”Ŧ Chimeric Detective Report

Comprehensive Analysis of Chimeric Contigs in Viral Metagenomic Assembly

28
Contigs Analyzed
7
Contigs Split
2
Contigs Preserved
0.66
Mean Confidence

📊 Summary Visualizations

Chimera Type Distribution

Confidence Score Distributions

Decision Summary

Evidence Types Overview

🔍 Detailed Analysis Results

Contig ID Chimera Type Confidence Decision Breakpoint Evidence Types Explanation
contig_003 technical_artifact 0.8 SPLIT 3122 gc_content_shift, kmer_composition_change
Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,122, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.33) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_013 technical_artifact 0.5 PRESERVE 2922 gc_content_shift, kmer_composition_change
Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,922, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
chimeric_001 technical_artifact 0.7 SPLIT 1356 gc_content_shift, kmer_composition_change
Contig chimeric_001 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,356, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.30) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
chimeric_004 technical_artifact 0.7 SPLIT 1488 gc_content_shift, kmer_composition_change
Contig chimeric_004 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,488, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.32) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
cov_chimeric_003 technical_artifact 0.5 PRESERVE 926 gc_content_shift, kmer_composition_change
Contig cov_chimeric_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 926, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_009 technical_artifact 0.5 SPLIT 4890 gc_content_shift, kmer_composition_change
Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,890, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.33) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.75.
contig_018 technical_artifact 0.7 SPLIT 1585 gc_content_shift, kmer_composition_change
Contig contig_018 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,585, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.34) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_005 technical_artifact 0.8 SPLIT 6302 gc_content_shift, kmer_composition_change
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,302, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_013 technical_artifact 1.0 PRESERVE 380 gc_content_shift, kmer_composition_change
Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 380, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.23) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_005 technical_artifact 0.5 SPLIT 4175 gc_content_shift, kmer_composition_change
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,175, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.16) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_003 technical_artifact 0.5 SPLIT 5713 gc_content_shift, kmer_composition_change
Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 5,713, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.13) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_005 technical_artifact 0.5 SPLIT 3474 gc_content_shift, kmer_composition_change
Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,474, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.20) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_006 technical_artifact 0.8 SPLIT 2229 gc_content_shift, kmer_composition_change
Contig contig_006 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,229, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.21) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_009 technical_artifact 0.8 SPLIT 6261 gc_content_shift, kmer_composition_change
Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,261, there is a 1.3x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.75.

📈 Individual Contig Details

Click on the links below to view detailed analysis for each chimeric contig:

â„šī¸ Methodology & Interpretation

Detection Methods

Chimeric contigs are detected using multiple complementary approaches:

  • Coverage Discontinuities: Sharp changes in read coverage depth
  • Sequence Composition: Changes in GC content and k-mer frequencies
  • Taxonomic Classification: Transitions between different viral/host lineages
  • Read Pair Orientation: Inconsistent paired-end read orientations

Classification Categories

  • Technical Artifacts: Assembly errors, typically split
  • PCR Chimeras: Amplification artifacts, typically split
  • Biological Recombination: Genuine recombination events, preserved
  • Provirus Integration: Virus-host integration sites, flagged

Confidence Scores

Confidence scores range from 0-1, with higher scores indicating stronger evidence for the classification. Scores above 0.8 are considered high confidence, 0.5-0.8 medium confidence, and below 0.5 low confidence.